VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jul 25 2006 - 12:41:53 CDT

Sergio,
  You can change the active color scale to any of the built
in scales Red->White->Blue, Blue->White->Red, etc, with the
color by volume method. I think many people use the RWB scale
for potential maps. The color scale control is found in the color
window.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jul 24, 2006 at 12:21:32PM -0500, Sergio Urahata wrote:
> Thank you again, Axel and John.
>
> I am looking into your suggestions. I am using
> version 1.8.4 under Windows XP with an ATI X700 video card.
>
> Regarding the resolution, I will re-run my code again with
> an increased number of grid cells. This may do the trick (I would need
> to do this anyway because there are way to many zero's
> on it, leading me with an useless huge file). I must say that even
> the medium resolution is not bad since the color range is
> very clear on the clipping plane. My only grip is the color of this plane
> which is always blue (using any color ID/User coloring option),
> red (with Charge/Volume) or "multicolor" (with Pos). White would
> be the best way to see the cutting layers.
>
> S.
>
> Obs. Axel, I do not mind sharing this data but right now the file
> uses almost 80MB. As soon as I get it smaller, I can upload it
> there.
>
>
>
> On 7/24/06, John Stone <johns_at_ks.uiuc.edu> wrote:
> >
> >Sergio,
> > Actually there are quite a few ways to show embedded surfaces, but
> >transparency does indeed have limitations (for all programs). You can
> >either use the colorID method, or you could color by volume, and set
> >the color scale colors using a Hue/Intensity/Saturation ramp (to make them
> >change more obviously than using a simple RWB color scale for example),
> >and you can clamp the color scale data range values (see trajectory tab)
> >to get better control over how it is displayed. As far as the resolution
> >of the resulting image, the color by volume method is calculated either by
> >"nearest voxel" (the low quality option), or by trilinear interpolation
> >(the "medium" option). Better yet would be a cubic interpolation of some
> >sort, but at present the graphics boards aren't quite there yet, which is
> >why we don't have a "high" option. Ultimately, the resolution of the
> >coloring
> >you get is determined by the combination of the original volumetric grid
> >resolution, and the largest texture map size your video card supports.
> >In the new versions of VMD, if your video card cannot load the full
> >resolution
> >texture map, VMD will automatically downsample it to a lower resolution.
> >If you're getting a poor quality 3-D texturing result, the most likely
> >reason is due to limitations with your video card, so long as you're sure
> >that your original potential map data is high resolution...
> >
> > John
> >
> >On Mon, Jul 24, 2006 at 11:28:07AM -0500, Sergio Urahata wrote:
> >> Thank you for the message, Axel.
> >>
> >> The reason I was playing with the transparency option
> >> is related to the way the data is distributed. If I just use color ID
> >> for each volume, it is not possible to see these distinct regions, since
> >> they are embebbed in each other.
> >>
> >> Your second suggestion solves this problem but there is one
> >> bug on the Clip Tool. The "Distance" bar does not move and
> >> the number on its side does not change, no matter
> >> whether the "Keep Aligned with Screen" is selected or not.
> >>
> >> I then tried to render the volumes using Volume Slice and
> >> the result is much better indeed. Do you know how to control
> >> the color of the slicing plane ? Also, is there a way to increase
> >> the quality of the projection ? (there only "low" and "medium" quality
> >> on the menu)
> >>
> >> Best,
> >>
> >> S.
> >>
> >>
> >> On 7/23/06, Axel Kohlmeyer <akohlmey_at_cmm.chem.upenn.edu> wrote:
> >> >
> >> >On Sat, 22 Jul 2006, Sergio Urahata wrote:
> >> >
> >> >SU> Hi all,
> >> >
> >> >hi sergio,
> >> >
> >> >SU> I have one PLT file which represents a 3D grid of volumetric data.
> >> >SU> VMD allows to render only specific isovalues, which is great.
> >> >SU> Would it be possible to set different colors for specific isovalues
> >?
> >> >
> >> >yes, you just create multiple isovalue representations and
> >> >assign a different color to each of them (via ColorID colorization).
> >> >
> >> >SU> This way, one could show where to find higher densities (or whatever
> >> >the
> >> >SU> mean each cell has) hence adding an interesting function for
> >> >SU> the "transparent" material option.
> >> >
> >> >i don't think so. the colors on the 'outside' would tint
> >> >whatever is 'inside'. what you may want to look into would
> >> >be a volume slice with Volume colorization, perhaps in
> >> >combination with multiple isosurfaces and a clipplane.
> >> >
> >> >regards,
> >> > axel.
> >> >
> >> >SU> I have selected many "Coloring" methods and "Volume" was the only
> >> >SU> one which changed the surface color (but still does not use
> >> >SU> the isovalues).
> >> >SU>
> >> >SU> Thank you,
> >> >SU>
> >> >SU> Sergio
> >> >SU>
> >> >SU>
> >> >
> >> >--
> >> >=======================================================================
> >> >Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> >> > Center for Molecular Modeling -- University of Pennsylvania
> >> >Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
> >> >tel: 1-215-898-1582, fax: 1-215-573-6233, office-tel: 1-215-898-5425
> >> >=======================================================================
> >> >If you make something idiot-proof, the universe creates a better idiot.
> >> >
> >> >
> >>
> >>
> >> --
> >> ========================================================
> >> Sergio Urahata, Ph.D.
> >> Biochemistry, Box 8231 Phone: (314) 362-4198(O)
> >> Washington University (314) 454-9209(H)
> >> 660 South Euclid Ave Fax: (314) 362-7183
> >> St. Louis, MO 63110 http://dasher.wustl.edu
> >> ========================================================
> >
> >--
> >NIH Resource for Macromolecular Modeling and Bioinformatics
> >Beckman Institute for Advanced Science and Technology
> >University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> >Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> >
>
>
> --
> ========================================================
> Sergio Urahata, Ph.D.
> Biochemistry, Box 8231 Phone: (314) 362-4198(O)
> Washington University (314) 454-9209(H)
> 660 South Euclid Ave Fax: (314) 362-7183
> St. Louis, MO 63110 http://dasher.wustl.edu
> ======================================================== 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078